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DrYak / GSoD_V-pipe_tutWW.md
Created March 31, 2024 06:30
Google Season of Docs - Better V-pipe tutorial for virus variant surveillance in wastewater

Better V-pipe tutorial for virus variant surveillance in wastewater

About V-pipe

The Computational Biology Group of ETH Zürich (CBG-ETHZ), member of the Swiss Institute of Bioinformatics (SIB), has developed the SIB Software Resource V-pipe: an Apache-licensed computational pipeline for the analysis of virus next-generation sequencing (NGS) data, specializing in samples of mixed viral populations.

This bioinformatics workflow has important applications in several different settings:

  • In clinical virology, information about the detection and quantification of viral quasispecies in a single patient sample can assist clinicians in the optimization of the treatment for this patient.
  • In clinical epidemiology, sequencing test samples during a viral outbreak provides information about the viral variants found in the population, which helps better understanding of the epidemic dynamics and gui
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DrYak / notes.md
Created November 3, 2023 09:23
NOTES running MeSS with LIMBO
@DrYak
DrYak / vp-ninjaturtles-howto.md
Last active May 19, 2023 13:09
V-pipe ninjaturtles HOWTO

Notes for the Wastewater experimental branch

Versions

  • 2023-05-19 - fixed an error in command for generating report (TSV => CSV).

General notes

  • Currently still experimental/work-in-progress
@DrYak
DrYak / dehuman.bsub
Last active October 4, 2021 21:00
Remove human reads from raw reads
#!/bin/bash
#BSUB -L /bin/bash
#BSUB -J COVID-dehumanize
#BSUB -M 6144
#BSUB -n 16
#BSUB -R rusage[mem=6144]
#BSUB -R span[hosts=1]
#BSUB -W 1420
# 4096 ; 235
@DrYak
DrYak / vpipe-sarsvoc2-tut.sh
Last active April 3, 2020 10:05
Testing V-pipe SARS-CoV-2
mkdir V-test
cd V-test
######################
### ###
### Miniconda3 ###
### ###
######################
@DrYak
DrYak / vpipe-tut.sh
Last active March 28, 2020 09:34
testing V-pipe
mkdir V-test
cd V-test
######################
### ###
### Miniconda3 ###
### ###
######################
@DrYak
DrYak / make_local_report.pl
Last active September 30, 2019 11:07
experimental local haplotype report
#!/usr/bin/env perl
use strict;
use Encode;
my $path = 'support';
my $report_html = <<'END_MESSAGE';
<!DOCTYPE html>
@DrYak
DrYak / shorah-tut.sh
Created September 10, 2019 15:00
testing recent shorah directly from github
mkdir -p ~/shorah-test
cd ~/shorah-test
#
# install bioconda
#
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
@DrYak
DrYak / patch-system-img.sh
Last active January 24, 2023 12:44
Patcher to add Mapsv1 into squashfs system.img for AlienDalvik on Sailfish OS'
#!/bin/bash
echo -e "\e[34;1m=================================\e[37;1m"
echo "[**] 0. Check environment"
echo -e "\e[34;1m=================================\e[0m"
if [ -e /opt/alien/system.img ]; then
HAS_ALIEN_DALVIK=1
ALIEN_VERSION="$(rpm -qf '/opt/alien/system.img' --qf '%{version}')"
echo "AlienDalvik image version ${ALIEN_VERSION} found"
@DrYak
DrYak / gist:81f73fff0d572130ff9d
Created April 24, 2015 22:24
disphelper patch - for wine and byref support - split source
diff --git a/source/convert.c b/source/convert.c
index ae61fe4..0c85ef9 100644
--- a/source/convert.c
+++ b/source/convert.c
@@ -25,13 +25,13 @@
#include <math.h>
/* Number of 100 nannosecond units in a FILETIME day */
-static const LONGLONG FILE_TIME_ONE_DAY = 864000000000;
+static const LONGLONG FILE_TIME_ONE_DAY = 864000000000LL;